基于高通量测序的中国水仙根际土壤微生物群落组成

李媛媛; 张琼; 陈小煌; 张敬虎; 陆銮眉

doi:10.19303/j.issn.1008-0384.2021.08.012

基于高通量测序的中国水仙根际土壤微生物群落组成

doi: 10.19303/j.issn.1008-0384.2021.08.012

1.
闽南师范大学生物科学与技术学院/闽台特色园林植物福建省高等学校重点实验室，福建　漳州　363000
2.
闽南师范大学化学化工与环境学院，福建　漳州　363000

基金项目: 福建省科技计划对外合作重点项目（2018I0014）；漳州市自然科学基金项目（ZZ2020J10）；漳州市科技重大专项（ZZ2019ZD01）；闽南师范大学校长基金项目（4206/L21918）

详细信息

作者简介:
李媛媛（1989−），女，博士，讲师，主要从事环境微生物学研究（E-mail：liyuanyuan9215@163.com）

通讯作者:
陆銮眉（1968−），女，教授，主要从事观赏园艺学研究（E-mail：358070295@qq.com）

中图分类号: S 682
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- 被引次数: 0
出版历程
- 收稿日期: 2021-03-28
- 修回日期: 2021-05-21
- 刊出日期: 2021-08-28

High-throughput Sequencing on Microbial Community in Rhizosphere Soil of Chinese Narcissus

1.
Provincial Key Laboratory of Landscape Plants with Fujian and Taiwan Characteristics/College of the Bioscience and Technology, Minnan Normal University, Zhangzhou, Fujian　363000, China
2.
College of the Chemistry, Chemical Engineering and Environment, Minnan Normal University, Zhangzhou, Fujian　363000, China

摘要

摘要: 目的明确中国水仙植株根际土壤微生物群落的组成特征。方法采用Illumina Miseq高通量测序技术对水仙根际土壤微生物样品的保守基因区进行测序及生物信息学分析，阐明中国水仙根际土壤的细菌、真菌和古菌群落结构组成，并对水仙根际土壤微生物的优势菌属进行深入分析。结果共获得优化序列175 840条，基于97%序列相似度，聚类为2 680个OTUs。优势细菌类群是绿弯菌门 Chloroflexi（30.86%）和变形菌门 Proteobacteria（20.67%），真菌以子囊菌门 Ascomycota（84.94%）为主，属水平上球毛壳菌 Chaetomium globosum（28.15%）和散子囊菌 Eurotiales（25.01%）占较高比例。古菌类群主要为奇古菌门 Thaumarchaeota（51.40%）、深古菌门 Bathyarchaeota（25.98%）和广古菌门 Euryarchaeota（20.65%）。其中，来自奇古菌门的SCG类群（25.67%）和嗜酸性氨氧化古菌 Candidatus_Nitrosotalea（12.93%）占较高比例。结论中国水仙根际土壤微域具有丰富多样的微生物类群，这对于开发和利用水仙根际土壤微生物资源具有重要意义。
- 中国水仙 /
- 根际土壤微生物 /
- 高通量测序 /
- 细菌 /
- 真菌 /
- 古菌
Abstract: Objective The microbial community in rhizosphere soils of Chinese narcissuses was analyzed. Method The Illumina Miseq high-throughput sequencing technology was used to obtain the relevant conserved gene regions of the microbes in soil specimens from Chinese narcissus planting lots. The community structures and distributions of dominant species of bacteria, fungi, and archaea in the rhizosphere soils were analyzed. Result In total, 175 840 optimized sequences were obtained and clustered from the specimens into 2 680 representative OTUs with a 97% similarity. The dominant bacteria were Chloroflexi (30.86%) and Proteobacteria (20.67%). Among the fungi, Ascomycota (84.94%) significantly overshadowed the others, with Chaetomium globosum (28.15%) and Ascomycetes (25.01%) accounted for the greater proportions. On archaea, Thaumarchaeota (51.40%), Bathyarchaeota (25.98%), and Euryarchaeota (20.65%) were the major phyla that had 25.67% SCG and 12.93% acidophilic ammonia oxidizing members. Conclusion The rhizosphere soils of Chinese narcissuses harbored diverse and rich microbial species. The information obtained would aid the development and utilization of the natural resources.
- Chinese narcissuses /
- rhizosphere soil microorganisms /
- high-throughput sequencing /
- bacteria /
- fungi /
- archaea

HTML全文

图 1 中国水仙根际微生物群落丰富度分布

Figure 1. Relative abundance of microorganisms in Chinese narcissus rhizosphere soil at phylum level

下载: 全尺寸图片幻灯片

图 2 中国水仙根际Top15微生物属水平上丰富度分布

Figure 2. Relative abundance of microorganisms in Chinese narcissus rhizosphere soil at genus level

下载: 全尺寸图片幻灯片

表 1 中国水仙根际土壤微生物高通量测序数据及其多样性指数

Table 1. Summarized high-throughput sequences and diversity index of microorganisms in Chinese narcissus rhizosphere soil

微生物类型 Microorganism Type	测序序列数 Total sequence number	平均序列长度 Mean length/bp	OTUs （97%）	代表 OTUs	Chao 指数	Ace 指数	香农均匀度 Shannon evenness	辛普森均匀度 Simpson evenness	香农多样性指数 Shannon diversity index	辛普森多样性指数 Simpson diversity index
细菌 Bacteria	39 188	413.7	29 447	2 453	3 089	3 133	0.845 0	0.125 8	6.595 8	0.003 2
真菌 Fungi	66 216	381.8	49 162	109	109	109	0.523 8	0.056 6	2.455 1	0.162 0
古菌 Archaea	70 436	428.5	44 517	118	118	118	0.544 2	0.078 6	2.596 6	0.107 8

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参考文献(49)

[1]	CHAPARRO J M, BADRI D V, VIVANCO J M. Rhizosphere microbiome assemblage is affected by plant development [J]. ISME Journal, 2014, 8(4): 790−803. doi: 10.1038/ismej.2013.196
[2]	MENDES R, GARBEVA P, RAAIJMAKERS J M. The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms [J]. FEMS Microbiology Reviews, 2013, 37(5): 634−663. doi: 10.1111/1574-6976.12028
[3]	BARDGETT R D, CARUSO T. Soil microbial community responses to climate extremes: Resistance, resilience and transitions to alternative states [J]. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 2020, 375(1794): 20190112. doi: 10.1098/rstb.2019.0112
[4]	王鑫鑫, 杨珍珍, 周婉柔, 等. 水仙根围细菌群落组成 [J]. 微生物学通报, 2017, 44(5):1081−1088. WANG X X, YANG Z Z, ZHOU W R, et al. Identification of rhizosphere bacterial communities of Narcissus tazetta [J]. Microbiology China, 2017, 44(5): 1081−1088.(in Chinese)
[5]	杨明俊, 李娟, 王永刚, 等. 水仙内生真菌的分离鉴定及聚类分析 [J]. 中草药, 2014, 6(11):1625−1630. YANG M J, LI J, WANG Y G, et al. Isolation and cluster analysis of endophytic fungi in Narcissus tazetta var. chinensis [J]. Chinese Herbal Medicines, 2014, 6(11): 1625−1630.(in Chinese)
[6]	RYU C M, FARAG, MOHAMED A, et al. Bacterial volatiles promote growth in Arabidopsis [J]. Proceedings of the National Academy of Sciences of the United States of America, 2003, 100(8): 4927−4932. doi: 10.1073/pnas.0730845100
[7]	MENDES R, KRUIJT M, DE BRUIJIN I, et al. Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria [J]. Science, 2011, 332(6033): 1097−1100. doi: 10.1126/science.1203980
[8]	HU J, WEI Z, FRIMAN V P, et al. Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression [J]. American Society for Microbiology, 2016, 7(6): e01790−16.
[9]	黄秋斌, 张颖, 刘凤英, 等. 蜡样芽孢杆菌B3-7在大田小麦根部的定殖动态及其对小麦纹枯病的防治效果 [J]. 生态学报, 2014, 34(10):2559−2566. HUANG Q B, ZHANG Y, LIU F Y, et al. Colonization dynamics of Bacillus cereus B3-7 on wheat roots and control efficiency against sharp eyespot of wheat [J]. Acta Ecologica Sinica, 2014, 34(10): 2559−2566.(in Chinese)
[10]	杨光柱, 黄文静, 李云国, 等. 苹果根腐病根际土壤真菌组成及多样性研究 [J]. 果树学报, 2020, 37(6):875−881. YANG G Z, HUANG W J, LI Y G, et al. Fungal community and diversity in rhizospheric soil with root rot in an apple orchard [J]. Journal of Fruit Science, 2020, 37(6): 875−881.(in Chinese)
[11]	李得铭, 翟子翔, 邓涛, 等. 番茄青枯菌分离与三重PCR体系建立 [J]. 分子植物育种, 2020, 18(11):209−215. LI D M, ZHAI Z X, DENG T, et al. Isolation of ralstonia solanacearum and establishment of triple PCR system [J]. Molecular Plant Breeding, 2020, 18(11): 209−215.(in Chinese)
[12]	BACH E M, WILLIAMS R J, HARGREAVES S K, et al. Greatest soil microbial diversity found in micro-habitats [J]. Soil Biology and Biochemistry, 2018, 118: 217−226. doi: 10.1016/j.soilbio.2017.12.018
[13]	钱宝, 刘凌, 肖潇. 土壤有机质测定方法对比分析 [J]. 河海大学学报(自然科学版), 2011, 39(1):34−38. QIAN B, LIU L, XIAO X. Comparative tests on different methods for content of soil organic matter [J]. Journal of Hohai University (Natural Sciences Edition), 2011, 39(1): 34−38.(in Chinese)
[14]	马丹. 凯氏定氮法测定食品中蛋白质含量 [J]. 计量与测试技术, 2008, 35(6):57−58. doi: 10.3969/j.issn.1004-6941.2008.06.030 MA D. Kjeldahl determination of protein content [J]. Measurement and Testing Technology, 2008, 35(6): 57−58.(in Chinese) doi: 10.3969/j.issn.1004-6941.2008.06.030
[15]	叶祥盛, 赵竹青. 流动注射法与碱解扩散法测定土壤有效氮的比较 [J]. 安徽农业科学, 2011, 20:12166−12167, 12178. doi: 10.3969/j.issn.0517-6611.2011.20.073 YE X S, ZHAO Z Q. Comparison of soil available nitrogen concentration between flow injection method and alkali-diffusion method [J]. Journal of Anhui Agricultural Sciences, 2011, 20: 12166−12167, 12178.(in Chinese) doi: 10.3969/j.issn.0517-6611.2011.20.073
[16]	BOWMAN R A, COLE C V. An exploratory method for fractionation of organic phosphorus from grassland soils [J]. Soil science, 1978, 125(2): 95−101. doi: 10.1097/00010694-197802000-00006
[17]	SIMARD R R. Ammonium acetate-extractable elements. In Soil sampling and methods of analysis[M]. Lewis Publisher: Boca Raton, FL, USA, 1993(1): 39-42.
[18]	MEIER L P, KAHR G. Determination of the cation exchange capacity (CEC) of clay minerals using the complexes of copper(II) ion with triethylenetetramine and tetraethylenepentamine [J]. Clays and Clay Minerals, 1999, 47(3): 386−388. doi: 10.1346/CCMN.1999.0470315
[19]	梁淑轩, 孙汉文. 石墨炉原子吸收光谱法分析药用植物中微量营养元素的含量 [J]. 光谱学与光谱分析, 2002, 22(5):847−849. doi: 10.3321/j.issn:1000-0593.2002.05.042 LIANG S X, SUN H W. Determination of trace elements in medicinal plants by Grapphite Furnace atomic absorption spectrometry [J]. Spectroscopy and Spectral Analysis, 2002, 22(5): 847−849.(in Chinese) doi: 10.3321/j.issn:1000-0593.2002.05.042
[20]	CHEN C, ZHANG J N, LU M, et al. Microbial communities of an arable soil treated for 8 years with organic and inorganic fertilizers [J]. Biology and Fertility of Soils, 2016, 52(4): 455−467. doi: 10.1007/s00374-016-1089-5
[21]	LI B X, CHEN H L, LI N N, et al. Spatio-temporal shifts in the archaeal community of a constructed wetland treating river water [J]. The Science of the Total Environment, 2017, 605/606: 269−275. doi: 10.1016/j.scitotenv.2017.06.221
[22]	ZHAO S C, QIU S J, XU X P, et al. Change in straw decomposition rate and soil microbial community composition after straw addition in different long-term fertilization soils [J]. Applied Soil Ecology, 2019, 138: 123−133. doi: 10.1016/j.apsoil.2019.02.018
[23]	BOLGER A M, LOHSE M, USADEL B, et al. Trimmomatic: a flexible trimmer for Illumina sequence data [J]. Bioinformatics, 2014, 30(15): 2114−2120. doi: 10.1093/bioinformatics/btu170
[24]	MAGOČ T, SALZBERG S L. FLASH: fast length adjustment of short reads to improve genome assemblies [J]. Bioinformatics, 2011, 27(21): 2957−2963. doi: 10.1093/bioinformatics/btr507
[25]	EDGAR R C. UPARSE: highly accurate OTU sequences from microbial amplicon reads [J]. Nature Methods, 2013, 10(10): 996−998. doi: 10.1038/nmeth.2604
[26]	LAN Y M, WANG Q, COLE J R, et al. Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms [J]. PLoS One, 2012, 7(3): e32491. doi: 10.1371/journal.pone.0032491
[27]	QUAST C, PRUESSE E, YILMAZ P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools [J]. Nucleic Acids Research, 2013, 41(D1): D590−D596.
[28]	SCHLOSS P D, WESTCOTT S L, RYABIN T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities [J]. Applied and Environmental Microbiology, 2009, 75: 7537−7541. doi: 10.1128/AEM.01541-09
[29]	伍海兵, 张青青, 梁晶. 城市绿地土壤肥力质量综合评价方法初探 [J]. 土壤通报, 2020, 51(4):795−800. WU H B, ZHANG Q Q, LIANG J. A comprehensive evaluation method of soil fertility quality in urban green space [J]. Chinese Journal of Soil Science, 2020, 51(4): 795−800.(in Chinese)
[30]	赖焕雄, 郑小琴. 漳州市近48年气候变化特征分析 [J]. 安徽农业科学, 2010, 38(15):8056−8060. doi: 10.3969/j.issn.0517-6611.2010.15.129 LAI H X, ZHENG X Q. Characteristics of climate change in Zhangzhou City in Recent 48 years [J]. Journal of Anhui Agricultural Sciences, 2010, 38(15): 8056−8060.(in Chinese) doi: 10.3969/j.issn.0517-6611.2010.15.129
[31]	DAVIS K E R, SANGWAN P, JANSSEN P H. Acidobacteria, Rubrobacteridae and Chloroflexi are abundant among very slow-growing and mini-colony-forming soil bacteria [J]. Environmental Microbiology, 2011, 13(3): 798−805. doi: 10.1111/j.1462-2920.2010.02384.x
[32]	FAN K K, DELGADO-BAQUERIZO M, GUO X S, et al. Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment [J]. The ISME Journal, 2021, 15: 550−561. doi: 10.1038/s41396-020-00796-8
[33]	HAN Q, MA Q, CHEN Y, et al. Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean [J]. The ISME Journal, 2020, 14(8): 1915−1928. doi: 10.1038/s41396-020-0648-9
[34]	WALTERS W A, JIN Z, YOUNGBLUT N, et al. Large-scale replicated field study of maize rhizosphere identifies heritable microbes [J]. PNAS, 2018, 115(28): 7368−7373. doi: 10.1073/pnas.1800918115
[35]	XU J, ZHANG Y, ZHANG P, et al. The structure and function of the global citrus rhizosphere microbiome [J]. Natural Communication, 2018, 9(1): 4894. doi: 10.1038/s41467-018-07343-2
[36]	雷旭, 李冰, 李晓, 等. 复合垂直流人工湿地系统中不同植物根际微生物群落结构 [J]. 生态学杂志, 2015, 34(5):1373−1381. LEI X, LI B, LI X, et al. Rhizosphere microbial community of three plants in vertical-flow constructed wetland [J]. Chinese Journal of Ecology, 2015, 34(5): 1373−1381.(in Chinese)
[37]	杨美玲, 张霞, 王绍明, 等. 基于高通量测序的裕民红花根际土壤细菌群落特征分析 [J]. 微生物学通报, 2018, 45(11):2429−2438. YANG M L, ZHANG X, WANG S M, et al. High throughput sequencing analysis of bacterial communities in Yumin safflower [J]. Microbiology China, 2018, 45(11): 2429−2438.(in Chinese)
[38]	CHEN S J, ZHU Y, SHAO T Y, et al. Relationship between rhizosphere soil properties and disease severity in highbush blueberry (Vaccinium corymbosum) [J]. Applied Soil Ecology, 2019, 127: 187−194.
[39]	GAO L, WANG R, GAO J M, et al. Analysis of the structure of bacterial and fungal communities in disease suppressive and disease conducive tobacco-planting soils in China [J]. Soil Research, 2019, 58(1): 35−40.
[40]	QI G F, CHEN S, KE L X, et al. Cover crops restore declining soil properties and suppress bacterial wilt by regulating rhizosphere bacterial communities and improving soil nutrient contents [J]. Microbiological Research, 2020, 238: 126505. doi: 10.1016/j.micres.2020.126505
[41]	TEDERSOO L, BAHRAM M, PÕLME S, et al. Global diversity and geography of soil fungi [J]. Science, 2014, 346(6213): 1078.
[42]	EGIDI E, DELGADO-BAQUERIZO M, PLETT J M, et al. A few Ascomycota taxa dominate soil fungal communities worldwide [J]. Nature Communication, 2019, 10: 2369. doi: 10.1038/s41467-019-10373-z
[43]	PIETRO A D, RELLA M G, PACHLATKO J P, et al. Role of antibiotics produced by Chaetomium globosum in biocontrol of Pythium ultimum, a causal agent of damping-off [J]. Physiology and Biochemistry, 1992, 8(2): 131−135.
[44]	PARK J H, CHOI G J, JANG K S, et al. Antifungal activity against plant pathogenic fungi of chaetoviridins isolated from Chaetomium globosum [J]. FEMS Microbiology Letters, 2005, 252(2): 309−313. doi: 10.1016/j.femsle.2005.09.013
[45]	ANGEL R, SOARES M I M, UNGAR E D, et al. Biogeography of soil Archaea and bacteria along a steep precipitation gradient [J]. The ISME Journal, 2010, 4(4): 553−563. doi: 10.1038/ismej.2009.136
[46]	HONG J K, CHO J C. Environmental variables shaping the ecological niche of thaumarchaeota in soil: Direct and indirect causal effects [J]. PLoS One, 2015, 10(8): e0133763. doi: 10.1371/journal.pone.0133763
[47]	SHAO K Q, JIANG X Y, HU Y, et al. Thaumarchaeota affiliated with Soil Crenarchaeotic Group are prevalent in the alkaline soil of an alpine grassland in northwestern China [J]. Annals of Microbiology, 2019, 69(8): 867−870. doi: 10.1007/s13213-019-01492-5
[48]	JIAO S, XU Y Q, ZHANG J, et al. Environmental filtering drives distinct continental atlases of soil Archaea between dryland and wetland agricultural ecosystems [J]. Microbiome, 2019, 7(1): 1−13. doi: 10.1186/s40168-018-0604-3
[49]	段昌海, 张翠景, 孙艺华, 等. 新型产甲烷古菌研究进展 [J]. 微生物学报, 2019, 59(6):981−995. DUAN C H, ZHANG C J, SUN Y H, et al. Recent advances on the novel methanogens [J]. Acta Microbiologica Sinica, 2019, 59(6): 981−995.(in Chinese)